With computations providing the ability to interpret innovative
laboratory studies, water divulged some of its secrets

It’s in the oceans, rivers and lakes, the sky,
bathtubs and drinking glasses. For most of us, water is a
taken-for-granted part of our lives. Nevertheless, after more
than a century of scientific study, water still holds many
secrets.

Ken Jordan, University of Pittsburgh

Photo: Justin Merriman, Pittsburgh Tribune-Review

“Water has properties that differ from any other
substance,” says Ken Jordan,
professor of chemistry at the University of Pittsburgh,
“and these properties play an important role in enabling
life as we know it. Just one example is that water has a very
high ability to store heat energy, otherwise day-night and
seasonal temperatures would fluctuate much more radically than
they do. We still don’t fully understand what makes water
so effective at this.”

Water divulged a few of its secrets in 2004, with Science magazine
listing a flurry of scientific papers on water’s structure
and chemical behavior as among the top 10 scientific
breakthroughs of the year. These new findings, said
Science, “could reshape fields from chemistry to
atmospheric sciences.”

Jordan collaborated on a number of these projects, and also
in follow-up studies reported this year. He’s a specialist
in theoretical and computational chemistry, well known for his
work on water clusters —groups of water molecules linked
together. “There are huge gaps in our
understanding,” he says, “of how water molecules
interact with each other.” For much of the work cited in
Science, Jordan and his team at Pitt relied on Rachel,
PSC’s 128-processor HP Marvel, a system well suited for
the quantum-level computations involved.

“There’s two common themes in these
projects,” says Jordan. “One is water. The other is
the power of computer modeling when coupled with
state-of-the-art experimental studies.” Several of these
projects explore long-standing questions about what happens when
an extra electron or proton interacts with water clusters,
changes that can affect many chemical processes. In all these
projects, Jordan’s computational work has complemented and
added to what can be learned in the laboratory.

Spectral Signatures

Vibrational spectroscopy is a powerful tool for identifying
subtle differences in molecular structure. Much like middle-C on
the piano vibrates at a higher frequency than the B below it,
different arrangements of molecules vibrate at different
frequencies.

In clusters of water molecules, vibrational spectroscopy can
register subtle differences in how the H2Os link up with each
other. Clustering occurs through “hydrogen bonds”
— links between hydrogen of one water molecule and oxygen
of another. Weaker than the covalent bonds that yoke two
hydrogens and an oxygen to form water, hydrogen bonds happen as electronic
charges — positive for hydrogen, negative for oxygen
— on different water molecules interact.

Inevitably some of the hydrogens are left dangling —
and these, as you might expect, vibrate at higher frequency than
the hydrogens involved in a hydrogen bond. Due to these
differences, each of many possible configurations for the same
number of water molecules has its own vibrational frequencies,
its “spectral signature” — which can be
determined with sensitive laboratory techniques.

From a sample of water clusters of the same mass at low
temperature, Jordan’s collaborators at the University of
Georgia and Yale University record spectral signatures. The
challenge then is to interpret them. “Is the experiment
seeing the global minimum?” says Jordan. “Or is it
probing an ensemble of many low-energy structures?” To
address that question, Jordan’s team applies theory and
calculates “the global minimum” — the
geometrical arrangement that has the lowest potential energy.
This structure is the most stable arrangement of the cluster and
the one that most populates the vibrational frequency spectra at
low temperature.

To find the global minimum, however, is easier said than
done. For a cluster of 21 waters, Jordan estimates there are
easily 1020 minima — that’s 100 million-trillion
possible structures that may form transiently, of which only one
is the global minimum. Even years of computing on the
world’s most powerful system wouldn’t be enough to
calculate the frequencies of all these structures.

Jordan’s team first uses “model
potentials” to identify a reduced set of structures that
comprise the likely candidates for global minimum. “You
can’t possibly examine all the minima,” explains
Jordan. “We have a research effort in our group to develop
fast algorithms that survey the landscape.” Within this
reduced set, they then use quantum-chemistry methods to
calculate frequencies. “We can then see which calculated
spectrum agrees best with the experimental spectrum.”

Wet Electrons, Protons & Magic Numbers

The Magic Number

This graphic, representing recent findings by Jordan and
collaborators, shows water’s magic number cluster as a
dodecahedron with the proton on the surface. Twenty H2O molecules are
bound together by hydrogen bonds (dotted lines). One H2O (purple) is in
the center of dodecahedral cage, and the excess proton is associated
with an H3O+ ion on the surface (blue).

This ability — practical only with advanced systems
like Rachel — to look at a large number of minima and
compute the associated vibrational spectra, which can then be
related to laboratory data, has made possible many of the new
findings about water. One of the questions that recent work has
addressed is the nature of the “wet electron.”

Also called the hydrated electron, this phenomenon —
an extra electron added to water — has been widely studied
because of its importance in “electron transfer”
processes in photosynthesis and in the body, where electrons
flit molecule-to-molecule, sparking the reactions of metabolism.
Most of what’s been known about the wet electron involves
bulk water — as opposed to clusters. New work by several
experimental groups used sophisticated spectroscopic methods to
analyze an extra electron attached to water clusters. These
studies developed information at a level of detail beyond
what’s been possible before. Some of this work relied on
computational studies by Jordan’s group.

Another of water’s mysteries has been the structure of
“magic number” clusters. Mass spectrometry shows
that a cluster of 21 water molecules — with one extra
proton (H+) — is much more stable than clusters with
either 20 or 22 water molecules. “There’s something
imparting special stability,” says Jordan, “and
that’s often associated with a special geometrical
arrangement.” Studies over the past 30 years have
postulated a dodecahedron, a cage of 20 water molecules, with an
H2O in the middle. But where’s the extra proton? Does it
go with the central H2O or on the surface of the cluster?

Using Rachel, among other computational resources,
Jordan’s student Richard Christie did calculations to
complement laboratory teams at Yale and the University of
Georgia. “There were these exciting experimental
results,” says Jordan, “and the question was how to
explore the needed range of structures quickly enough to rapidly
publish a joint experimental/theoretical paper.” Running
on 16 of Rachel’s processors required about two days of
computing to arrive at spectral signatures for one minima.

The results have settled the question. The magic number
proton is on the surface. “This debate has been going on
for many years,” says Jordan, “but we’ve found
pretty definitely that the proton sits on the surface of the
dodecahedron.” This answer, as is usual, brings new
problems to resolve. “There’s still a question about
how fast the proton can move around. It’s not a finished
story.”

Better understanding of the “magic number” cluster
may help to unleash a major source of untapped energy

Methane Hydrate

Much of the natural gas on Earth is created from organic
deposits on the ocean floor and held there in crystalline
structures of frozen water up to 100 meters thick. Known as
methane hydrate, these crystals form from dodecahedral clusters
of water (red & white, dotted lines show hydrogen bonds), which
create a cage around a single methane molecule (CH4, gray &
white). This same arrangement of waters forms the “magic number”
cluster. The water lattice for these hydrates often includes two
types of cages (blue & magenta).

Resolving questions about the magic-number cluster, notes
Jordan, has implications for a major source of untapped energy.
Methane hydrates — a structure that includes dodecahedral
cages of water enclosing molecules of methane, aka natural gas.
Research in the last decade has found that huge deposits of
methane hydrate lie on the ocean floor, and there are major
research efforts underway to find how to harness this methane.
Jordan’s group is working with four laboratory groups in
California looking at relationships between water clusters and
the similarly structured gas hydrates.

In 2005, as a follow-up to their 2004 report on the
magic-number cluster, Jordan and his collaborators at Georgia
and Yale published exciting results involving an extra proton in
smaller water clusters, often referred to as the “hydrated
proton.” Research over many years identified two competing
arrangements. “One,” says Jordan, “is where
the proton is associated with a single water molecule, and that
gives H3O+ — often called the Eigen form, for
the Nobel scientist who proposed it. The other form is with the
proton equally shared between two waters —
H5O2+, called Zundel.”

With innovative spectroscopic techniques and Jordan’s
calculations to interpret the data, the researchers for the
first time identified clear spectral signatures for the two
structures. By adding water molecules one by one, they found
striking shifts in the frequencies — indications of
movement back and forth between the Eigen and Zundel forms as
well as the importance of structures that are intermediate
between these two limiting forms.

“It gives us a handle,” says Jordan, “on
how sensitive the spectra are to the environment.” The
extra proton is fundamental to the chemistry of acids and this
finding, which no one expected, has wide implications. What
especially intrigues Jordan is that when water reveals secrets
it seems to hint at even deeper ones. “To me that’s
the most interesting science — when you discover hidden
questions you didn’t anticipate when you started.”